Hi Stefano,
Can you try out what we put together:
https://github.com/modENCODE-DCC/Galaxy
Thanks,
Q
On Thu, Feb 14, 2013 at 8:28 PM, stefano cardinale
s.cardin...@berkeley.edu wrote:
Hi, I am having a problem with running galaxy on the Amazon cloud. I have
tried this several times over

On Sep 12, 2012, at 1:00 PM, David Hoover wrote:
Are there any environment variables that are honored by toolshed installed
tools? I tried creating a tool that uses ${GALAXY_DATA_INDEX_DIR} or
$GALAXY_HOME, then uploaded it the test toolshed, then installed it
automatically. Neither of

Stefano,
Sounds like it's most likely that the security groups aren't configured
correctly. What I'd recommend would be to launch your instance using
http://usegalaxy.org/cloudlaunch which does all of those configuration steps
for you automatically.
-Dannon
On Feb 14, 2013, at 8:28 PM,

Now try running the test data in Galaxy to see if you get the same results. You
should probably try running from the history first and then try adding the test
data as a built-in genome via the bowtie2_indexes.loc table
Best,
J.
On Feb 15, 2013, at 12:18 AM, Sachit Adhikari wrote:
Hi Jeremy,

This is not a known bug. For questions related to Tophat errors, you might try
the Tophat mailing list:
tophat.cuffli...@gmail.com
Good luck,
J.
On Feb 15, 2013, at 6:02 AM, Sachit Adhikari wrote:
Galaxy is working fine in command line whereas in Galaxy at last i got this
error:

Jeremy,
But the tophat2 is running successfully in the command line. So, I guess
it's related to Galaxy. Why am I getting this error in Galaxy? Is it
because I don't have latest Galaxy? Is it file permission issue? I am using
Tophat V2.0.7 and latest Bowtie2 version.
On Fri, Feb 15, 2013 at 8:02

The wrapper you are using is for MACS 1.3, there is a wrapper that is
compatible with 1.4 in the toolshed.
--
James Taylor, Assistant Professor, Biology/CS, Emory University
On Fri, Feb 15, 2013 at 9:26 AM, greg margeem...@gmail.com wrote:
Hi guys,
I'm trying to run MACS in my local galaxy

Thanks! So one question, when I go to install it from the toolshed I
see two choices for a revision to select:
3:cdd9791c0afa
0:c1eeccec29d1
Which would I choose and why?
Thanks,
Greg
On Fri, Feb 15, 2013 at 9:30 AM, James Taylor ja...@jamestaylor.org wrote:
The wrapper you are using is for

You likely want the newest version (3)
On Feb 15, 2013 9:37 AM, greg margeem...@gmail.com wrote:
Thanks! So one question, when I go to install it from the toolshed I
see two choices for a revision to select:
3:cdd9791c0afa
0:c1eeccec29d1
Which would I choose and why?
Thanks,
Greg
On

Hello Greg,
What version of Galaxy are you running - it is likely older than the December
20, 2012 Galaxy release. You'll have to upgrade to at least that release to
use the main Galaxy tool shed.
Greg Von Kuster
On Feb 15, 2013, at 9:43 AM, greg wrote:
Hi guys,
I'm getting an error

Thanks.
I'm trying to follow the instructions here to update the code:
http://wiki.galaxyproject.org/Admin/Get%20Galaxy#Keep_your_code_up_to_date
But I'm getting this error:
hg incoming
Not trusting file /misc/local/galaxy/galaxy-dist/.hg/hgrc from
untrusted user galaxy, group scicomp
Not

I still haven't heard back from the Bio-Linux guys regarding how to update
Galaxy within Bio-Linux...
In the meantime, I tried to play with the Manage data libraries, in order
to import large datasets. I modified the library_import_dir line in the
universe_wsgi.ini. The first thing I can say is

Hi,
Enclosed is a dataset that I am not able to see anymore.
I don't see any error in the log (but maybe I missed it !).
To answer to Carlos, I have the problem with Firefox and Chrome.
Cheers,
Mathieu
- Mail original -
De: Dannon Baker dannon.ba...@gmail.com
À: Mathieu Bahin

Thank you Greg,
That what I tried to do initially but I could not find this tool the tool shed
repository. Here is what I did, as an admin I went to Search and browse shed
tool-Galaxy main tool shed
Then I searched for ngsrich I could not find it. Then I looked under static
category I still

Hi guys,
I'm trying to do my first update on my local galaxy install (it's been
a few months at least since I installed)
I'm trying to follow the instructions here to update the code:
http://wiki.galaxyproject.org/Admin/Get%20Galaxy#Keep_your_code_up_to_date
My first question is how do I roll

It's really hard to say what's going on with those issues without more
information about the particular version of galaxy (which
unfortunately we'd get from `hg tip`, which won't work on your bio
linux install) or proxy configuration, if any. I'm also not sure what
the appropriate bio linux

On Feb 15, 2013, at 10:45 AM, greg wrote:
Hi guys,
I'm trying to do my first update on my local galaxy install (it's been
a few months at least since I installed)
I'm trying to follow the instructions here to update the code:

Hello Peter, please see my response at the end.
On Feb 15, 2013, at 6:47 AM, Peter Cock wrote:
On Sep 12, 2012, at 1:00 PM, David Hoover wrote:
Are there any environment variables that are honored by toolshed installed
tools? I tried creating a tool that uses ${GALAXY_DATA_INDEX_DIR} or

Well, (un)fortunately this file works for me in both firefox and
chrome on the current galaxy-dist. Just to confirm -- when you click
the eye, it doesn't download the file either, right -- nothing at all
happens?
In chrome, could you open the console (Tools - Javascript Console or
Ctrl+Shift+J)

Hello Hakeem,
When searching the tool shed from Galaxy, only repositories that are
automatically installable into Galaxy will be located. Repositories are
considered installable if they contain valid Galaxy utilities (tools,
proprietary datatypes, repository dependency definitions, tool

Thanks! One followup, see below.
-Greg
On Fri, Feb 15, 2013 at 11:01 AM, Nate Coraor n...@bx.psu.edu wrote:
On Feb 15, 2013, at 10:45 AM, greg wrote:
Migrate:
% sh manage_db.sh upgrade
Pay attention to whatever the first revision you are migrating from is.
Probably 109 if you were at

Hi,
I hope this is the right place to ask,
I am trying to rsync from:
rsync -avzP rsync://datacache.g2.bx.psu.edu/indexes/
and I am getting the error:
@ERROR: chroot failed
rsync error: error starting client-server protocol (code 5) at main.c(1534)
[Receiver=3.0.9
I know I can rsync to any

On Fri, Feb 15, 2013 at 4:05 PM, Greg Von Kuster g...@bx.psu.edu wrote:
Hi guys,
Reading the rest of the thread from December, Greg's new code did
get checked in and should be working (I've not tried this yet).
However, I can't help feeling that defining the two environment variables
David

Hi Peter,
On Feb 15, 2013, at 11:14 AM, Peter Cock wrote:
On Fri, Feb 15, 2013 at 4:05 PM, Greg Von Kuster g...@bx.psu.edu wrote:
Hi guys,
Reading the rest of the thread from December, Greg's new code did
get checked in and should be working (I've not tried this yet).
However, I can't

Thank you Greg,
I will contact the owner of that software and see if we can get it installed.
Regards
From: Greg Von Kuster [mailto:g...@bx.psu.edu]
Sent: Friday, February 15, 2013 10:13 AM
To: Hakeem Almabrazi
Cc: Galaxy Dev
Subject: Re: [galaxy-dev] Install NGSRich in local galaxy
Hello

On Fri, Feb 15, 2013 at 11:08 AM, Dannon Baker dannon.ba...@gmail.com wrote:
Well, (un)fortunately this file works for me in both firefox and
chrome on the current galaxy-dist. Just to confirm -- when you click
the eye, it doesn't download the file either, right -- nothing at all
happens?

On Fri, Feb 15, 2013 at 6:10 PM, Nicola Soranzo sora...@crs4.it wrote:
Peter wrote:
It seems to have confused the bitbucket page a little, but I have
checked in your initial wrapper to my development repository (I
use the tools branch):